Variant report

Variant	rs553798
Chromosome Location	chr5:49540130-49540131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11514621	0.81[AMR][1000 genomes]
rs11742067	0.81[AMR][1000 genomes]
rs13358828	0.82[AMR][1000 genomes]
rs2125456	0.82[AMR][1000 genomes]
rs2168920	0.82[AMR][1000 genomes]
rs2199089	0.81[AMR][1000 genomes]
rs2199090	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2199092	0.81[AMR][1000 genomes]
rs2219451	0.83[AMR][1000 genomes]
rs2219452	0.83[AMR][1000 genomes]
rs2352789	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4321782	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4554275	0.83[AMR][1000 genomes]
rs481222	0.83[AMR][1000 genomes]
rs485101	0.83[AMR][1000 genomes]
rs4865637	0.81[AMR][1000 genomes]
rs496108	0.83[ASN][1000 genomes]
rs498951	0.84[ASN][1000 genomes]
rs504520	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs528968	0.82[AMR][1000 genomes]
rs531198	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs534123	0.82[AMR][1000 genomes]
rs535100	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs535113	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs547563	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs552892	0.84[AMR][1000 genomes]
rs559096	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs577482	0.81[ASN][1000 genomes]
rs8185347	0.81[AMR][1000 genomes]
rs8188210	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:37 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv820439	chr5:49405763-49552643	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv15107	chr5:49405763-49562327	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv2760950	chr5:49432831-49624358	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv598089	chr5:49441601-49547088	ZNF genes & repeats Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598091	chr5:49441966-49547088	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv598093	chr5:49455285-49547088	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1034318	chr5:49455624-49542837	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1028131	chr5:49455624-49552686	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1017682	chr5:49455624-49556126	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1033820	chr5:49455624-49560281	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1025722	chr5:49455624-49561216	ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1016253	chr5:49455624-49564818	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1034447	chr5:49455624-49568948	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1015794	chr5:49455624-49572706	ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1021120	chr5:49455624-49583553	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1034906	chr5:49455624-49586503	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1016533	chr5:49455624-49587789	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv1033970	chr5:49455624-49595874	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv1032046	chr5:49455624-49597527	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv1021477	chr5:49455624-49624358	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1019539	chr5:49455624-49702736	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
22	nsv1023402	chr5:49455624-49708458	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
25	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	nsv598096	chr5:49462228-49547088	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv598097	chr5:49468722-49549410	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
28	nsv598099	chr5:49479708-49549410	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv598102	chr5:49492838-49547088	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv598104	chr5:49499290-49547088	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv598105	chr5:49503299-49547088	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
32	nsv598106	chr5:49507498-49549410	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
33	esv3376641	chr5:49528095-49550793	ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
34	esv3328813	chr5:49528095-49550993	ZNF genes & repeats Active TSS Enhancers Weak transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
35	esv3369422	chr5:49528095-49550993	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
36	esv3397392	chr5:49528595-49550793	ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
37	nsv598107	chr5:49530641-49560490	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs553798	EMB	cis	Thyroid	GTEx
rs553798	EMB	cis	Skin Sun Exposed Lower leg	GTEx
rs553798	EMB	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49529000-49550200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:49529600-49542200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
3	chr5:49529800-49542000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
4	chr5:49536600-49541600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:49539000-49549400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr5:49539200-49541400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:49540000-49541400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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